Background correction

Background was estimated by median filter with quite large kernel (51x51 px). To correct the background, we substructed estimaded median value from the original image. Please note that background estimate calculation are slow. (For the stationary computer one frame takes approximately 4 minutes) The result for particular Omero image ID presented below.

This procedure works good only till approximately 48 frames (4 hours), then the biofilm structure exceed (51x51) kernel and require background correction with larger kernel.

Viz images before and after correction

Plot intensity profiles across central vertical line